niwrap-freesurfer 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_extract_fcd_features.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_EXTRACT_FCD_FEATURES_METADATA = Metadata(
-    id="4dc97ce09339ae602c500d2ce62f291dceb53709.boutiques",
+    id="822940a66948e150cdf82461b3ef67a0620a6fc0.boutiques",
     name="mri_extract_fcd_features",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ MRI_EXTRACT_FCD_FEATURES_METADATA = Metadata(
 
 
 MriExtractFcdFeaturesParameters = typing.TypedDict('MriExtractFcdFeaturesParameters', {
-    "__STYXTYPE__": typing.Literal["mri_extract_fcd_features"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_extract_fcd_features"]],
+    "subject": str,
+    "hemi": str,
+    "output_file": InputPathType,
+    "subjects_dir": typing.NotRequired[str | None],
+})
+MriExtractFcdFeaturesParametersTagged = typing.TypedDict('MriExtractFcdFeaturesParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_extract_fcd_features"],
     "subject": str,
     "hemi": str,
     "output_file": InputPathType,
     "subjects_dir": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_extract_fcd_features": mri_extract_fcd_features_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class MriExtractFcdFeaturesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_extract_fcd_features(...)`.
+    Output object returned when calling `MriExtractFcdFeaturesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def mri_extract_fcd_features_params(
     hemi: str,
     output_file: InputPathType,
     subjects_dir: str | None = None,
-) -> MriExtractFcdFeaturesParameters:
+) -> MriExtractFcdFeaturesParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +56,7 @@ def mri_extract_fcd_features_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_extract_fcd_features",
+        "@type": "freesurfer/mri_extract_fcd_features",
         "subject": subject,
         "hemi": hemi,
         "output_file": output_file,
@@ -105,13 +81,13 @@ def mri_extract_fcd_features_cargs(
     """
     cargs = []
     cargs.append("mri_extract_fcd_features")
-    cargs.append(params.get("subject"))
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("output_file")))
-    if params.get("subjects_dir") is not None:
+    cargs.append(params.get("subject", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("output_file", None)))
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "sdir",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
     return cargs
 
@@ -137,9 +113,11 @@ def mri_extract_fcd_features_outputs(
 
 def mri_extract_fcd_features_execute(
     params: MriExtractFcdFeaturesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriExtractFcdFeaturesOutputs:
     """
+    mri_extract_fcd_features
+    
     A tool for extracting focal cortical dysplasia features.
     
     Author: FreeSurfer Developers
@@ -148,10 +126,12 @@ def mri_extract_fcd_features_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriExtractFcdFeaturesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EXTRACT_FCD_FEATURES_METADATA)
     params = execution.params(params)
     cargs = mri_extract_fcd_features_cargs(params, execution)
     ret = mri_extract_fcd_features_outputs(params, execution)
@@ -167,6 +147,8 @@ def mri_extract_fcd_features(
     runner: Runner | None = None,
 ) -> MriExtractFcdFeaturesOutputs:
     """
+    mri_extract_fcd_features
+    
     A tool for extracting focal cortical dysplasia features.
     
     Author: FreeSurfer Developers
@@ -183,21 +165,19 @@ def mri_extract_fcd_features(
     Returns:
         NamedTuple of outputs (described in `MriExtractFcdFeaturesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_EXTRACT_FCD_FEATURES_METADATA)
     params = mri_extract_fcd_features_params(
         subject=subject,
         hemi=hemi,
         output_file=output_file,
         subjects_dir=subjects_dir,
     )
-    return mri_extract_fcd_features_execute(params, execution)
+    return mri_extract_fcd_features_execute(params, runner)
 
 
 __all__ = [
     "MRI_EXTRACT_FCD_FEATURES_METADATA",
     "MriExtractFcdFeaturesOutputs",
-    "MriExtractFcdFeaturesParameters",
     "mri_extract_fcd_features",
+    "mri_extract_fcd_features_execute",
     "mri_extract_fcd_features_params",
 ]

niwrap_freesurfer/freesurfer/mri_extract_label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_EXTRACT_LABEL_METADATA = Metadata(
-    id="12bb0b0e9b903975a24f0391cea338580ba40fd4.boutiques",
+    id="ec009de70ff2bd413e2325fc17f72a2ba0554c5c.boutiques",
     name="mri_extract_label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MRI_EXTRACT_LABEL_METADATA = Metadata(
 
 
 MriExtractLabelParameters = typing.TypedDict('MriExtractLabelParameters', {
-    "__STYXTYPE__": typing.Literal["mri_extract_label"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_extract_label"]],
+    "input_volume": InputPathType,
+    "labels": list[str],
+    "output_name": str,
+    "gaussian_smoothing": typing.NotRequired[float | None],
+    "transform_file": typing.NotRequired[InputPathType | None],
+    "exit_none_found": bool,
+    "dilate": typing.NotRequired[float | None],
+    "erode": typing.NotRequired[float | None],
+})
+MriExtractLabelParametersTagged = typing.TypedDict('MriExtractLabelParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_extract_label"],
     "input_volume": InputPathType,
     "labels": list[str],
     "output_name": str,
@@ -24,43 +35,11 @@ MriExtractLabelParameters = typing.TypedDict('MriExtractLabelParameters', {
     "dilate": typing.NotRequired[float | None],
     "erode": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_extract_label": mri_extract_label_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "mri_extract_label": mri_extract_label_outputs,
-    }.get(t)
 
 
 class MriExtractLabelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_extract_label(...)`.
+    Output object returned when calling `MriExtractLabelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def mri_extract_label_params(
     exit_none_found: bool = False,
     dilate: float | None = None,
     erode: float | None = None,
-) -> MriExtractLabelParameters:
+) -> MriExtractLabelParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +75,7 @@ def mri_extract_label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_extract_label",
+        "@type": "freesurfer/mri_extract_label",
         "input_volume": input_volume,
         "labels": labels,
         "output_name": output_name,
@@ -128,30 +107,30 @@ def mri_extract_label_cargs(
     """
     cargs = []
     cargs.append("mri_extract_label")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.extend(params.get("labels"))
-    cargs.append(params.get("output_name"))
-    if params.get("gaussian_smoothing") is not None:
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.extend(params.get("labels", None))
+    cargs.append(params.get("output_name", None))
+    if params.get("gaussian_smoothing", None) is not None:
         cargs.extend([
             "-s",
-            str(params.get("gaussian_smoothing"))
+            str(params.get("gaussian_smoothing", None))
         ])
-    if params.get("transform_file") is not None:
+    if params.get("transform_file", None) is not None:
         cargs.extend([
             "-t",
-            execution.input_file(params.get("transform_file"))
+            execution.input_file(params.get("transform_file", None))
         ])
-    if params.get("exit_none_found"):
+    if params.get("exit_none_found", False):
         cargs.append("-exit_none_found")
-    if params.get("dilate") is not None:
+    if params.get("dilate", None) is not None:
         cargs.extend([
             "-dilate",
-            str(params.get("dilate"))
+            str(params.get("dilate", None))
         ])
-    if params.get("erode") is not None:
+    if params.get("erode", None) is not None:
         cargs.extend([
             "-erode",
-            str(params.get("erode"))
+            str(params.get("erode", None))
         ])
     return cargs
 
@@ -171,16 +150,18 @@ def mri_extract_label_outputs(
     """
     ret = MriExtractLabelOutputs(
         root=execution.output_file("."),
-        output_volume=execution.output_file(params.get("output_name")),
+        output_volume=execution.output_file(params.get("output_name", None)),
     )
     return ret
 
 
 def mri_extract_label_execute(
     params: MriExtractLabelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriExtractLabelOutputs:
     """
+    mri_extract_label
+    
     Extracts a set of labeled voxels from an image.
     
     Author: FreeSurfer Developers
@@ -189,10 +170,12 @@ def mri_extract_label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriExtractLabelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EXTRACT_LABEL_METADATA)
     params = execution.params(params)
     cargs = mri_extract_label_cargs(params, execution)
     ret = mri_extract_label_outputs(params, execution)
@@ -212,6 +195,8 @@ def mri_extract_label(
     runner: Runner | None = None,
 ) -> MriExtractLabelOutputs:
     """
+    mri_extract_label
+    
     Extracts a set of labeled voxels from an image.
     
     Author: FreeSurfer Developers
@@ -233,8 +218,6 @@ def mri_extract_label(
     Returns:
         NamedTuple of outputs (described in `MriExtractLabelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_EXTRACT_LABEL_METADATA)
     params = mri_extract_label_params(
         input_volume=input_volume,
         labels=labels,
@@ -245,13 +228,13 @@ def mri_extract_label(
         dilate=dilate,
         erode=erode,
     )
-    return mri_extract_label_execute(params, execution)
+    return mri_extract_label_execute(params, runner)
 
 
 __all__ = [
     "MRI_EXTRACT_LABEL_METADATA",
     "MriExtractLabelOutputs",
-    "MriExtractLabelParameters",
     "mri_extract_label",
+    "mri_extract_label_execute",
     "mri_extract_label_params",
 ]

niwrap_freesurfer/freesurfer/mri_extract_largest_cc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_EXTRACT_LARGEST_CC_METADATA = Metadata(
-    id="53c95adc4bc5ee58b6c612c01980a0da86b6de18.boutiques",
+    id="79eaca1d5ec3a60aab4032e9244e7e24b61917ab.boutiques",
     name="mri_extract_largest_CC",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRI_EXTRACT_LARGEST_CC_METADATA = Metadata(
 
 
 MriExtractLargestCcParameters = typing.TypedDict('MriExtractLargestCcParameters', {
-    "__STYXTYPE__": typing.Literal["mri_extract_largest_CC"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_extract_largest_CC"]],
+    "input_volume": InputPathType,
+    "output_volume": str,
+    "threshold": typing.NotRequired[float | None],
+    "hemisphere": typing.NotRequired[typing.Literal["lh", "rh"] | None],
+    "largest_cc_in_bg": bool,
+    "original_volume": typing.NotRequired[InputPathType | None],
+    "label_value": typing.NotRequired[float | None],
+})
+MriExtractLargestCcParametersTagged = typing.TypedDict('MriExtractLargestCcParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_extract_largest_CC"],
     "input_volume": InputPathType,
     "output_volume": str,
     "threshold": typing.NotRequired[float | None],
@@ -23,43 +33,11 @@ MriExtractLargestCcParameters = typing.TypedDict('MriExtractLargestCcParameters'
     "original_volume": typing.NotRequired[InputPathType | None],
     "label_value": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_extract_largest_CC": mri_extract_largest_cc_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "mri_extract_largest_CC": mri_extract_largest_cc_outputs,
-    }.get(t)
 
 
 class MriExtractLargestCcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_extract_largest_cc(...)`.
+    Output object returned when calling `MriExtractLargestCcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def mri_extract_largest_cc_params(
     largest_cc_in_bg: bool = False,
     original_volume: InputPathType | None = None,
     label_value: float | None = None,
-) -> MriExtractLargestCcParameters:
+) -> MriExtractLargestCcParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +71,7 @@ def mri_extract_largest_cc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_extract_largest_CC",
+        "@type": "freesurfer/mri_extract_largest_CC",
         "input_volume": input_volume,
         "output_volume": output_volume,
         "largest_cc_in_bg": largest_cc_in_bg,
@@ -124,29 +102,29 @@ def mri_extract_largest_cc_cargs(
     """
     cargs = []
     cargs.append("mri_extract_largest_CC")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(params.get("output_volume"))
-    if params.get("threshold") is not None:
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(params.get("output_volume", None))
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-T",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("hemisphere") is not None:
+    if params.get("hemisphere", None) is not None:
         cargs.extend([
             "-hemi",
-            params.get("hemisphere")
+            params.get("hemisphere", None)
         ])
-    if params.get("largest_cc_in_bg"):
+    if params.get("largest_cc_in_bg", False):
         cargs.append("-I")
-    if params.get("original_volume") is not None:
+    if params.get("original_volume", None) is not None:
         cargs.extend([
             "-O",
-            execution.input_file(params.get("original_volume"))
+            execution.input_file(params.get("original_volume", None))
         ])
-    if params.get("label_value") is not None:
+    if params.get("label_value", None) is not None:
         cargs.extend([
             "-L",
-            str(params.get("label_value"))
+            str(params.get("label_value", None))
         ])
     return cargs
 
@@ -166,16 +144,18 @@ def mri_extract_largest_cc_outputs(
     """
     ret = MriExtractLargestCcOutputs(
         root=execution.output_file("."),
-        output_volume_file=execution.output_file(params.get("output_volume")),
+        output_volume_file=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_extract_largest_cc_execute(
     params: MriExtractLargestCcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriExtractLargestCcOutputs:
     """
+    mri_extract_largest_CC
+    
     This program extracts the largest connected component of the input volume.
     
     Author: FreeSurfer Developers
@@ -184,10 +164,12 @@ def mri_extract_largest_cc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriExtractLargestCcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EXTRACT_LARGEST_CC_METADATA)
     params = execution.params(params)
     cargs = mri_extract_largest_cc_cargs(params, execution)
     ret = mri_extract_largest_cc_outputs(params, execution)
@@ -206,6 +188,8 @@ def mri_extract_largest_cc(
     runner: Runner | None = None,
 ) -> MriExtractLargestCcOutputs:
     """
+    mri_extract_largest_CC
+    
     This program extracts the largest connected component of the input volume.
     
     Author: FreeSurfer Developers
@@ -226,8 +210,6 @@ def mri_extract_largest_cc(
     Returns:
         NamedTuple of outputs (described in `MriExtractLargestCcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_EXTRACT_LARGEST_CC_METADATA)
     params = mri_extract_largest_cc_params(
         input_volume=input_volume,
         output_volume=output_volume,
@@ -237,13 +219,13 @@ def mri_extract_largest_cc(
         original_volume=original_volume,
         label_value=label_value,
     )
-    return mri_extract_largest_cc_execute(params, execution)
+    return mri_extract_largest_cc_execute(params, runner)
 
 
 __all__ = [
     "MRI_EXTRACT_LARGEST_CC_METADATA",
     "MriExtractLargestCcOutputs",
-    "MriExtractLargestCcParameters",
     "mri_extract_largest_cc",
+    "mri_extract_largest_cc_execute",
     "mri_extract_largest_cc_params",
 ]